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Old 08-09-2011, 05:54 AM   #1
Ori
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Default SRMA error

Hi,

First time using SRMA and right the way into error... typical.

Anyhow, here it is:
Code:
java -jar -Xmx2g ../srma-0.1.15.jar I=sorted.bam O=SRMA.bam R=chr17.fasta 

[Tue Aug 09 14:42:24 CEST 2011] srma.SRMA INPUT=[sorted.bam] OUTPUT=[SRMA.bam] REFERENCE=chr17.fasta    OFFSET=20 MIN_MAPQ=0 MINIMUM_ALLELE_PROBABILITY=0.1 MINIMUM_ALLELE_COVERAGE=3 MAXIMUM_TOTAL_COVERAGE=100 CORRECT_BASES=false USE_SEQUENCE_QUALITIES=true QUIET_STDERR=false MAX_HEAP_SIZE=8192 MAX_QUEUE_SIZE=65536 GRAPH_PRUNING=false NUM_THREADS=1 TMP_DIR=/tmp/ VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
Allele coverage cutoffs:
coverage: 1	minimum allele coverage: 0
coverage: 2	minimum allele coverage: 0
coverage: 3	minimum allele coverage: 0
coverage: 4	minimum allele coverage: 1
coverage: 5	minimum allele coverage: 1
coverage: 6	minimum allele coverage: 1
coverage: 7	minimum allele coverage: 2
coverage: 8	minimum allele coverage: 2
coverage: 9	minimum allele coverage: 3
coverage: >9	minimum allele coverage: 3
Records processsed: 1 (last 17:3217-3266)java.lang.Exception: Error.  Soft clipping with color-space data not currently supported.
	at srma.Align.align(Align.java:134)
	at srma.SRMA$AlignThread.run(SRMA.java:659)
Please report bugs to srma-help@lists.sourceforge.net
hmm...

help would be appreciated!

thanks
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Old 08-09-2011, 07:51 AM   #2
nilshomer
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The release does not support soft-clipping in color space data. There is an experimental branch in the GIT repository called "cs-soft" that you can test out. I am assuming you mapped with SHRiMP. If you cannot get soft-clipping to work, use BFAST or another mapper.
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Old 08-09-2011, 07:58 AM   #3
Ori
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Thanks for quick answer. I'll test "cs-soft".

For mapping I used novoalign.
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Old 08-16-2011, 02:55 AM   #4
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Little update:

"cs-soft" worked fine on novoalign produced bam file. By the way, I was compiling it with latest samtools jar instead of recommended older version. It worked.

Then I as well made alignment of same data using BFAST run it through SRMA.
I got quite a few error saying:

Code:
Exception in thread "main" java.lang.StackOverflowError
    at java.util.ArrayList$SubList.add(ArrayList.java:928)
As far as I remember that is due to too many recursions... Hmm.

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Old 08-16-2011, 07:52 AM   #5
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I am not sure how to do it (google would) but have you increased your stack size?
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Old 08-18-2011, 05:01 AM   #6
Ori
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StackOverflow error solved. In case anybody else runs in similar problem:

-Xss[amount of mem]m flag does the job.

Easy, when you know
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Old 08-19-2011, 08:09 AM   #7
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Excellent, thank-you for posting back your solution.
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